Contacts of the strand formed by residues 215 - 219 (chain D) in PDB entry 3NJ4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 215 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402B LEU 5.3 7.4 - - - +
213D GLY 4.8 4.7 - - - +
214D LYS* 1.3 73.6 - - - +
216D ALA* 1.3 60.5 + - - +
217D VAL* 4.9 0.4 - - + -
238D ARG* 3.2 44.2 - - + +
240D ILE* 4.0 26.7 - - + -
268D GLU* 3.6 23.8 - - + +
269D GLY* 3.5 3.0 - - - +
270D ASN* 2.7 49.6 + - - +
271D ILE 3.3 3.0 + - - -
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Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D LYS* 3.7 1.4 + - + -
215D VAL* 1.3 75.4 - - - +
217D VAL* 1.3 63.1 + - - +
218D VAL 4.1 0.2 - - - -
232D LEU* 3.7 36.1 - - + -
237D ALA* 4.7 6.1 - - + -
238D ARG 2.8 11.2 + - - +
239D VAL* 3.2 10.5 - - + +
240D ILE* 2.8 25.5 + - - +
271D ILE* 3.4 23.6 - - + -
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Residues in contact with VAL 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D VAL* 4.9 2.7 - - + -
216D ALA* 1.3 76.8 - - - +
218D VAL* 1.3 66.4 + - - +
219D ALA* 4.1 1.7 + - + +
240D ILE* 3.5 16.2 - - + +
242D THR* 4.4 12.1 - - + -
262D MET* 4.1 18.2 - - + -
265D ALA* 3.8 35.4 - - + +
269D GLY* 3.8 25.6 - - - +
271D ILE 2.9 6.3 + - - -
272D PHE* 3.6 15.9 - - + -
273D VAL* 2.9 28.4 + - - +
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Residues in contact with VAL 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D VAL* 1.3 79.4 - - - +
219D ALA* 1.3 63.2 + - - +
220D GLY 3.5 18.0 + - - +
225D GLY* 4.1 13.5 - - - +
228D CYS* 4.4 4.0 - - + -
229D ALA* 4.3 8.1 - - - +
232D LEU* 3.9 27.4 - - + -
239D VAL* 3.9 15.0 - - + -
240D ILE 2.8 9.3 + - - -
241D ILE* 3.4 17.4 - - + +
242D THR* 3.1 23.6 + - - +
273D VAL* 3.4 7.6 - - + +
275D THR* 3.7 21.5 - - + -
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Residues in contact with ALA 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D VAL* 4.1 2.1 + - + +
218D VAL* 1.3 71.6 - - - +
220D GLY* 1.3 53.4 + - - +
242D THR* 3.0 16.4 - - + +
262D MET* 5.6 5.6 - - - -
273D VAL 2.9 14.2 + - - +
274D THR* 4.0 7.9 - - + -
275D THR* 2.6 37.6 + - - -
276D THR* 3.5 8.8 + - - +
281D ILE* 3.5 31.9 - - + -
282D ILE* 6.1 0.2 - - + -
504D NAD 4.9 1.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il